You can define your tools, add them to the tool library, and then re-arrange them so the ones you most commonly use occupy the first ten tool library slots. Then, when you're working on a new project, you can just click 'Load Library to List" while in the Project Tools mode, which will copy the first ten tool definitions from your tool library to the current project automatically.
For the project size and origin all that matters is that you define a canvas volume that fits the cutpaths you want to generate - it doesn't have to be the same size as your workpiece but some people like to treat the canvas volume and its dimensions as their workpiece. The machine origin is relative to this volume - which is to say that wherever you want to zero your machine, relative to the generated toolpaths, is restricted to the canvas volume and its extents.
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